I believe that zombies and minor factions don't trigger events like raid engines or core cpa guard posts. Besides, zombies won't attack a planet until I do, so there shouldn't be to much trouble. Raid engine waves are regular waves, not zombies, so I should be able to zombify them.
I could be wrong about all of this though, but I'll find out soon enough. So far I'm about 3 hours ingame and got 6 planets... still alive and kicking. Botnet is repaired and fully functioning, so the zombies will come to my aid (or demise) very soon.
EDIT: I was right, zombies don't trigger the engine and engine waves can be zombified. Hooray for finding a botnet 4 hops from my homeworld. I just succesfully destroyed 3 raid engines in a row, using my botnet to deal with the waves. 3 and a half hours ingame and now I can finally grab my first shard lol.